Boolean Union Modifier Disappearing Components
No, Blender did not run out of memory. If it had, Blender would have crashed. Furthermore, the scale (applied or not) of an object has nothing to do with it's complexity. A mesh with 5000 polygons takes up exactly (within a few bits) the same RAM no matter what scale it is.

This is probably a bug. If you can reproduce it reliably, you should look for it in the bug tracker and if it hasn't already been reported, report it.